Cell-penetrating peptides (CPPs) are cationic peptides that are able to induce cellular uptake and delivery of large and hydrophilic molecules, that otherwise do not cross the plasma membrane of eukaryotic cells. Despite their potential use for gene transfer and drug delivery, the mode of action of CPPs is still mysterious. Nonetheless, the interaction with phospholipid bilayers constitutes the first step in the process. The interaction of two CPPs with distinct charge distribution, penetratin (nonamphipathic) and RL16 (a secondary amphipathic peptide with antimicrobial properties) with lipid membranes was investigated. For this purpose, we employed three independent techniques, comprising (31)P-nuclear magnetic resonance, differential scanning calorimetry (DSC), and plasmon waveguide resonance (PWR) spectroscopy. In view of the cationic nature of the peptides, their interaction and affinity for zwitterionic versus anionic lipids was investigated. Although a strong affinity was observed when negative charged lipids were present, the peptides' thermodynamic behavior on binding to zwitterionic versus anionic lipids and the induced supramolecular structure organization in those lipids was quite different. The study suggests that the amphipathic profile and charge distribution of CPPs strongly influences the perturbation mechanism of the peptide on the bilayer establishing the frontier between a pure CPP and a CPP with antimicrobial properties.